PDB-9h6s: Structure of the V606M/W622L mutant of myosin UNC-54

ID or keywords:

Entry

Database: PDB / ID: 9h6s

Title

Structure of the V606M/W622L mutant of myosin UNC-54

Components

Myosin-4

Keywords

MOTOR PROTEIN / Unc-54 / myosin

Function / homology

Function and homology information

egg-laying behavior / striated muscle myosin thick filament / skeletal muscle myosin thick filament assembly / muscle myosin complex / A band / myosin filament / locomotion / sarcomere organization / myosin II complex / structural constituent of muscle ...
Similarity search - Function

Biological species

Caenorhabditis elegans (invertebrata)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Arnese, R. / Meinhart, A. / Deszcz, L. / Clausen, T.

Funding support

1items

Citation

Journal: To Be Published
Title: Structure of the V606M/W622L mutant of myosin UNC-54
Authors: Arnese, R. / Meinhart, A. / Deszcz, L. / Clausen, T.

History

Deposition	Oct 25, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	May 6, 2026	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	9h6s.cif.gz	728.8 KB	Display	PDBx/mmCIF format
PDB format	pdb9h6s.ent.gz	504.9 KB	Display	PDB format
PDBx/mmJSON format	9h6s.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/h6/9h6s ftp://data.pdbj.org/pub/pdb/validation_reports/h6/9h6s	HTTPS FTP

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Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#18 - Jun 2001 Myosin similarity (13) #174 - Jun 2014 GFP-like Proteins similarity (8) #55 - Jul 2004 DNA Ligase similarity (1) #64 - Apr 2005 Kinesin similarity (1) #175 - Jul 2014 Microtubules similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

Deposited unit

A: Myosin-4

B: Myosin-4

hetero molecules

183 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Myosin-4

hetero molecules

defined by author
Evidence: gel filtration
91.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Myosin-4

hetero molecules

defined by author
91.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	91.033, 124.272, 96.957
Angle α, β, γ (deg.)	90.000, 109.878, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details (eV)
d_1	ens_1	(chain "A" and (resid 1 through 197 or resid 212 through 792))
d_2	ens_1	(chain "B" and resid 1 through 792)

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
d_1	1	MET	MET	SER	SER	A	A	1 - 197	1 - 197
d_1	2	VAL	VAL	HIS	HIS	A	A	212 - 792	212 - 792
d_2	1	MET	MET	HIS	HIS	B	B	1 - 792	1 - 792

NCS oper: (Code: givenMatrix: (0.827411976081, -0.560000283894, -0.0422977999071), (0.553731109193, 0.800947679221, 0.227738169533), (-0.0936551149203, -0.211854896541, 0.972803280351)Vector: 40. ...

#1: Protein	Myosin-4 / Myosin heavy chain B / MHC B / Uncoordinated protein 54 Mass: 91160.195 Da / Num. of mol.: 2 / Mutation: V606M W622L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Caenorhabditis elegans (invertebrata) / Gene: unc-54, myo-4, F11C3.3 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P02566
#2: Chemical	ChemComp-FMT / FORMIC ACID Mass: 46.025 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CH₂O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
Has protein modification	N

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.84 Å³/Da / Density % sol: 56.72 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 20% (w/v) PEG335, 200 mM sodium formate

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ESRF

/ Beamline: ID23-1 / Wavelength: 0.885603 Å

Detector

Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 25, 2024

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.885603 Å / Relative weight: 1

Reflection

Resolution: 2.159→77 Å / Num. obs: 103942 / % possible obs: 95.6 % / Redundancy: 3.64 % / B_iso Wilson estimate: 47.29 Å² / CC_1/2: 0.9858 / Net I/σ(I): 2.64

Reflection shell

Resolution (Å)	Num. unique obs	CC_1/2	Diffraction-ID
2.159-2.196	5384	0.1267	1
2.376-2.432	5410	0.3772	1

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Processing

Software

Name	Version	Classification
PHENIX	1.21.1_5286	refinement
XDS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.4→76.78 Å / SU ML: 0.3185 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.2374
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2401	3826	5.03 %
R_work	0.2119	72301	-
obs	0.2133	76127	96.08 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 58.26 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→76.78 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	12342	0	12	41	12395

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0029	12609
X-RAY DIFFRACTION	f_angle_d	0.6481	16983
X-RAY DIFFRACTION	f_chiral_restr	0.0444	1826
X-RAY DIFFRACTION	f_plane_restr	0.005	2206
X-RAY DIFFRACTION	f_dihedral_angle_d	17.6089	4774

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 1.02393528525 Å

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.4-2.43	0.375	151	0.3095	2689	X-RAY DIFFRACTION	99.06
2.43-2.46	0.3206	178	0.31	2750	X-RAY DIFFRACTION	99.29
2.46-2.5	0.3033	144	0.2974	2751	X-RAY DIFFRACTION	99.25
2.5-2.53	0.3071	158	0.2935	2748	X-RAY DIFFRACTION	99.05
2.53-2.57	0.3144	142	0.2854	2769	X-RAY DIFFRACTION	99.45
2.57-2.61	0.3107	155	0.2814	2747	X-RAY DIFFRACTION	99.45
2.61-2.65	0.2951	159	0.2706	2722	X-RAY DIFFRACTION	98.97
2.65-2.7	0.3164	88	0.2887	1513	X-RAY DIFFRACTION	54.36
2.7-2.75	0.275	131	0.2616	2788	X-RAY DIFFRACTION	99.52
2.75-2.8	0.2846	143	0.2587	2720	X-RAY DIFFRACTION	99.41
2.8-2.86	0.3165	132	0.2631	2837	X-RAY DIFFRACTION	99.7
2.86-2.92	0.3087	127	0.2508	2767	X-RAY DIFFRACTION	99.59
2.92-2.99	0.2672	141	0.2493	2742	X-RAY DIFFRACTION	99.59
2.99-3.06	0.2646	130	0.2516	2793	X-RAY DIFFRACTION	99.59
3.06-3.14	0.2704	146	0.2363	2814	X-RAY DIFFRACTION	99.7
3.14-3.24	0.2743	147	0.232	2765	X-RAY DIFFRACTION	99.73
3.24-3.34	0.2389	136	0.2315	2791	X-RAY DIFFRACTION	99.66
3.34-3.46	0.2698	102	0.2295	2003	X-RAY DIFFRACTION	72.14
3.46-3.6	0.2705	163	0.2256	2760	X-RAY DIFFRACTION	99.66
3.6-3.76	0.226	114	0.2022	2536	X-RAY DIFFRACTION	89.59
3.76-3.96	0.213	160	0.191	2439	X-RAY DIFFRACTION	88.7
3.96-4.21	0.1959	150	0.179	2771	X-RAY DIFFRACTION	99.9
4.21-4.54	0.2178	135	0.1751	2813	X-RAY DIFFRACTION	99.86
4.54-4.99	0.1911	144	0.1742	2804	X-RAY DIFFRACTION	99.86
4.99-5.71	0.2418	137	0.184	2829	X-RAY DIFFRACTION	100
5.71-7.2	0.215	165	0.2065	2776	X-RAY DIFFRACTION	99.73
7.2-76.78	0.1765	148	0.1549	2864	X-RAY DIFFRACTION	99.57

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°²)	L12 (°²)	L13 (°²)	L22 (°²)	L23 (°²)	L33 (°²)	S11 (Å °)	S12 (Å °)	S13 (Å °)	S21 (Å °)	S22 (Å °)	S23 (Å °)	S31 (Å °)	S32 (Å °)	S33 (Å °)	T11 (Å²)	T12 (Å²)	T13 (Å²)	T22 (Å²)	T23 (Å²)	T33 (Å²)	Origin x (Å)	Origin y (Å)	Origin z (Å)
1	2.70888705773	0.871537577627	0.507910306413	2.02202722382	0.591320095101	1.80770270171	0.0641599917002	0.318093259557	0.185355109754	-0.166775138205	0.0530743183987	-0.393724051978	0.0420569711307	0.238661740193	-0.123604126328	0.400821802655	0.0631803566274	0.0459198546141	0.429428466671	0.0491260149384	0.416678762568	52.9594489872	26.4758222504	15.9345938119
2	1.19017221439	-0.152594356928	0.300688945383	0.543973618363	0.0505289872561	1.12142833377	0.131861432903	0.155346701699	-0.135927238842	-0.0764135859977	-0.0376852410588	0.064655750598	0.159796043829	-0.299849786595	-0.0936942988403	0.430459185876	-0.0381299326307	0.0304458337514	0.467766288977	0.0336088568148	0.378420424406	15.6728416765	19.3679467849	9.75930809459
3	1.29383766521	0.0849463045579	0.262159220568	0.422864398462	-0.0252955826255	0.517854628703	0.0407933638224	-0.0106266073056	0.025190716445	0.0115799594414	0.00767038240302	-0.0374134318891	0.0543535424103	-0.0734943389956	-0.0610208455079	0.466154610192	0.00398521273296	0.0449472416468	0.409423285653	0.0165308802527	0.362928171905	32.315552669	27.8112765149	26.644993111
4	1.82309957962	0.630442662228	-0.0249515243673	2.73171200098	1.16084111932	2.3186653296	-0.150829013677	0.185687496556	0.31199127715	-0.303795728412	0.00281787887737	-0.0550041492882	-0.441068264494	0.136311566306	0.139698278566	0.435955036938	-0.047498859502	-0.0208286493501	0.366814299177	0.0314892463428	0.380962301766	69.0640525225	-20.5460401091	27.5729410284
5	1.40703850771	0.194455178359	0.281916701128	0.648093383154	0.236755340315	0.835678274381	0.0165644682342	0.10532982026	-0.0583986315476	-0.0228140656197	0.0643256129782	0.0910200725257	-0.0333847184828	-0.0801187172897	-0.102941925721	0.452902614388	-0.0183138700538	0.0461279393776	0.319257110871	0.0596627121706	0.3899202742	42.2091790708	-48.4467185722	26.4991091921
6	0.958855703748	0.365155179479	0.296285665526	0.55477879214	0.0368513378334	0.395465442785	-0.053899750905	0.0221766551166	0.0975516118769	0.101538003226	0.0514539558857	0.0237394350543	-0.0473322706276	-0.0587138440294	0.00556827211803	0.502419571293	0.0278415730747	0.065082271053	0.375728673045	0.0171649251954	0.418690464058	50.402165614	-29.0800152419	39.4105619493

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 149 )	A	A	1 - 149	1 - 149
2	2	chain 'A' and (resid 150 through 502 )	A	A	150 - 502	150 - 490
3	3	chain 'A' and (resid 503 through 794 )	A	A	503 - 794	491 - 767
4	4	chain 'B' and (resid 1 through 149 )	B	D	1 - 149	1 - 149
5	5	chain 'B' and (resid 150 through 502)	B	D	150 - 502	150 - 488
6	6	chain 'B' and (resid 503 through 792 )	B	D	503 - 792	489 - 763

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